20.309:Schedule

WEEK	LECTURES	LAB	READINGS & ASSIGNMENTS
	Electronics
0	Thursday, Sep. 7 Course Overview, procedures, syllabus, scheduling	Friday, Sep. 8, 3:00-4:00PM Lab orientation and tour, safety, introduction to electronics
1	Tuesday, Sep. 12 Electronics for DNA analysis; dividers, Thevenin's theorem, impedance and loading, RC circuits Thursday, Sep. 14 RC circuits: transfer functions, Laplace transforms, impedance, RC filters	Monday, Sep. 11 9:30-10:30AM Lab orientation and tour, safety, introduction to electronics Monday, Sep. 11 - Friday Sep. 15 Lab manual for Week 1: Intro to Electronics. Intro to DC measurements, dividers, impedance, photodiode i-v curves, AC measurements, transfer functions; the Wheatstone bridge for temperature measurement	Readings Resistors, capacitors, voltage & current dividers, RC transients. Impedance, frequency response, filters. This brief introduction to diodes will be helpful for working on the labs this week.
2	Tuesday, Sep. 19 Feedback: Black's formula, the loop; op-amps: "golden rules" and circuit examples Friday, Sep. 22 DNA analysis: SNP detection, chemical equilib. - K and deltaG; description of DNA melting lab apparatus	Monday, Sep. 18 - Friday Sep. 22 Lab manual for Weeks 2 & 3: Measuring DNA Melting Curves. Build optics for DNA melting experiment, build photodiode readout circuit; calibrate fluorescence signal Matlab Tutorial file 1 (the basics) Matlab Tutorial file 2 (curve fitting, etc.)	Readings Operational amplifiers.   HOMEWORK SET 1, due Friday, 9/22 by 12:00 noon. Homework Set 1 SOLUTIONS and associated Matlab files.
3	Tuesday, Sep. 26 Fourier series, integrals, Fourier transform (continuous/discrete) Thursday, Sep. 28 Fourier analysis (cont'd) Thursday, Sep. 28 @ 7:00pm – Room 56-614 Student presentations (Session #1)	NO LAB MONDAY SEP. 25 (Student holiday) Tuesday, Sep. 26 - Friday, Sep. 29 Lab manual for Weeks 2 & 3: Measuring DNA Melting Curves. Complete DNA melting curves apparatus; test perfect-match, all-mismatch, and single-base mismatch DNA strands	Readings Fourier Transforms. FFT reference material Thursday, Sep. 28 @ 7:00pm – Room 56-614 Student presentations (Session #1)
	Mechanics
4	Tuesday, Oct. 3 Scanning probe microscopy (and associated critical band audio files) Thursday, Oct. 5 Signals, noise, Power Spectral Density	Monday, Oct. 2 - Friday, Oct. 6 AFM alignment and calibration, AFM imaging I Lab Manual for weeks 4-6: The Atomic Force Microscope	Readings A helpful link that discusses spectral leakage when doing spectral analysis. See also the FFT reference reading   LAB REPORT #1 (Measuring DNA Melting Curves) due Friday, Oct. 6 by 12:00 noon.
5	NO LECTURE TUESDAY, OCT. 10 (Columbus Day) Thursday, Oct. 12 Correlation/convolution, lock-in amplification, linear systems	NO LAB MON-TUE (Columbus Day Weekend) Wednesday, Oct. 11 - Friday, Oct. 13 AFM imaging II; force spectroscopy Lab Manual for weeks 4-6: The Atomic Force Microscope	Readings Tutorial 1: Overview of Fourier Transforms Tutorial 2: Sampling and Aliasing One-page handout, with a few convolution clarification examples. HOMEWORK SET 2, due Wednesday, 10/11 by 12:00 noon.
6	Tuesday, Oct. 17 Equipartition theorem and thermal fluctuations Thursday, Oct. 19 Student Presentations (Session #2)	Monday, Oct. 16 - Friday Oct. 20 Thermal fluctuations of microcantilevers: Boltzmann's constant experiment Lab Manual for weeks 4-6: The Atomic Force Microscope	Lab Exercise on Sampling and Aliasing Thursday, Oct. 19 (in class) Student Presentations (Session #2)
	Optics
7	Tuesday, Oct. 24 Image processing I Thursday, Oct. 26 Image processing II	Monday, Oct. 23 - Friday, Oct. 27 Image processing Handout on Image Processing	Readings Great Matlab Matrix Indexing Tutorial Image Processing Readings (from Gonzalez & Woods): Chapter 4: histograms, contrast, spatial filtering. Chapter 8: morphology Chapter 7: segmentation Chapter 9: recognition & interpretation
8	Tuesday, Oct. 31 Physical optics and optical instrumentation: detectors, noise Thursday, Nov. 2 Optical instrumentation: sources, lasers	Monday, Oct. 30 - Friday, Nov. 3 Optoelectronics: PMT, & photon counting	LAB REPORT #2 (The Atomic Force Microscope) due Monday, Oct. 30 by 12:00 noon. HOMEWORK SET 3 due (Friday, Nov. 3 by 12:00noon).
9	Tuesday, Nov. 7 Intro to microscopy: geometric optics, lenses, ray tracing Thursday, Nov. 9 Fluorescence spectroscopy	Monday, Nov. 6 - Friday, Nov. 9 Fluorescence microscope construction I: lenses, white light imaging NO LAB FRIDAY NOV. 10 (Veteran's Day)
10	Tuesday, Nov. 14 interference and diffraction, phase-contrast miscroscopy Thursday, Nov. 16 Resolution in microscopy; Fourier optics	Monday, Nov. 13 - Friday, Nov. 17 Fluorescence microscope construction II, fluorescence imaging, live-cell imaging & microrheology	(evening date/time TBD) Student Presentations (Session #3)
11	Tuesday, Nov. 21 interference and diffraction, phase-contrast miscroscopy NO LECTURE THURSDAY, NOV. 23 (Thanksgiving)	Monday, Nov. 20 - Wednesday, Nov. 24 Light-scattering microscope and Fourier optics NO LAB THU-FRI (Thanksgiving Weekend)	LAB REPORT #3 due (date/time TBD).
12	Tuesday, Nov. 28 Optical trapping Thursday, Nov. 30 3D microscopy	Monday, Nov. 27 - Friday, Dec. 1 Optical trapping	(evening date/time TBD) Student Presentations (Session #4)
13	Tuesday, Dec. 5 3D image processing Thursday, Dec. 7	Monday, Dec. 4 - Friday, Dec. 8 3D Imaging & Visualization; confocal & two-photon microscopy, ImageJ
14	Tuesday, Dec. 12 Student presentations (Session #5)		Tuesday, Dec. 12 (in class) Student presentations (Session #5)